Flexible docking and refinement with a coarse-grained protein model using ATTRACT

A coarse-grained (CG) protein model implemented in the ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI Rounds 22-27. For six targets, acceptable or better quality solutions have been submitted corresponding to approximate to 60% of all targets. For one target, promising results on the prediction of the hydration structure at the protein-protein interface have been achieved. New approaches for the rapid flexible refinement have been developed based on a combination of atomistic representation of the bonded geometry and a CG description of nonbonded interactions. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed. Proteins 2013; 81:2167-2174. (c) 2013 Wiley Periodicals, Inc.